They also had the option of only replacing the defective parts at a parts + rate. A little cheaper, but them no everthing is replaced..... I went the total rebuild route myself.....

Fire up the motor last night for the first time this season. Fuel pump primed first turn of the key and motor fired like it had been stopped for just a few hours. Pleasant surprise.
I geuss my question goes back to my original question. Could I only be having this problem when the boat is being towed a long distance? My first thought was the vibration on the trailer without the system running might drain it back to the tank. Ill be trailering 3 hrs to run it this weekend so Ill see what happens.
Opinions on this are appreciated. I dont want to get stuck anywhere.

Trailered to Lake George this weekend and pump had a different problem. I nearly sh!t when I dropped the boat in and NO fuel pump activity. After a slight moment of panic I climbed in the hatch, wiggled a couple wires, tapped on the relay and vvrrom...started right up. Pump was already primed and fired immediatly. This relay has been replaced once already so Im sure its a weak link. This is not the problem I had last year which I wasnt able to duplicate.

Aeromotive suggested to me to run 10awg wire to the pump from the battery and put a remote relay near the pump. use the stock merc relay to energize the remote relay. This is to prevent the std merc relay from burning out and the voltage loss on the smaller stock wiring. They draw about 13-14 Amps and the wire is only 18 or 16 awg.

Raypanic,
Thank you, I will check wires and get back. I believe mine was set up with only one relay. This may be why Im burning them out.